GO analysis
For the 6hr timepoint
GO <- gopher(SucLow6hrs,url="athaliana", alpha=2)
## Loading required package: jsonlite
##
## Attaching package: 'jsonlite'
## The following object is masked from 'package:purrr':
##
## flatten
## No enrichments found in task: mapman
GO_SucLow6hrs <- GO$go
GO <- gopher(SucHigh6hrs,url="athaliana", alpha=2)
## No enrichments found in task: mapman
GO_SucHigh6hrs <- GO$go
GO <- gopher(PiLow6hrs, url="athaliana", alpha=2)
## No enrichments found in task: mapman
GO_PiLow6hrs <- GO$go
GO <- gopher(PiHigh6hrs, url="athaliana", alpha=2)
## No enrichments found in task: mapman
GO_PiHigh6hrs <- GO$go
GO <- gopher(AzdLow6hrs, url="athaliana", alpha=2)
## No enrichments found in task: mapman
GO_AzdLow6hrs <- GO$go
GO <- gopher(AzdHigh6hrs, url="athaliana", alpha=2)
## No enrichments found in task: mapman
GO_AzdHigh6hrs <- GO$go
GO <- gopher(AzdNPLow6hrs, url="athaliana", alpha=2)
## No enrichments found in task: mapman
GO_AzdNPLow6hrs <- GO$go
GO <- gopher(AzdNPHigh6hrs, url="athaliana", alpha=2)
## No enrichments found in task: mapman
GO_AzdNPHigh6hrs <- GO$go
GO <- gopher(AzdNSLow6hrs, url="athaliana", alpha=2)
## No enrichments found in task: mapman
GO_AzdNSLow6hrs <- GO$go
GO <- gopher(AzdNSHigh6hrs, url="athaliana", alpha=2)
## No enrichments found in task: mapman
GO_AzdNSHigh6hrs <- GO$go
For the 24hr timepoint
GO <- gopher(SucLow24hrs, url="athaliana", alpha=2)
## No enrichments found in task: mapman
GO_SucLow24hrs <- GO$go
GO <- gopher(SucHigh24hrs, url="athaliana", alpha=2)
## No enrichments found in task: mapman
GO_SucHigh24hrs <- GO$go
GO <- gopher(PiLow24hrs, url="athaliana", alpha=2)
## No enrichments found in task: mapman
GO_PiLow24hrs <- GO$go
GO <- gopher(PiHigh24hrs, url="athaliana", alpha=2)
## No enrichments found in task: mapman
GO_PiHigh24hrs <- GO$go
GO <- gopher(AzdLow24hrs, url="athaliana", alpha=2)
## No enrichments found in task: mapman
GO_AzdLow24hrs <- GO$go
GO <- gopher(AzdHigh24hrs, url="athaliana", alpha=2)
## No enrichments found in task: mapman
GO_AzdHigh24hrs <- GO$go
GO <- gopher(AzdNPLow24hrs, url="athaliana", alpha=2)
## No enrichments found in task: mapman
GO_AzdNPLow24hrs <- GO$go
GO <- gopher(AzdNPHigh24hrs, url="athaliana", alpha=2)
## No enrichments found in task: mapman
GO_AzdNPHigh24hrs <- GO$go
GO <- gopher(AzdNSLow24hrs, url="athaliana", alpha=2)
## No enrichments found in task: mapman
GO_AzdNSLow24hrs <- GO$go
GO <- gopher(AzdNSHigh24hrs, url="athaliana", alpha=2)
## No enrichments found in task: mapman
GO_AzdNSHigh24hrs <- GO$go
For Wouter’s data
GO <- gopher(Seedling_Low, url="athaliana", alpha=2)
## No enrichments found in task: mapman
GO_Seedling_Low <- GO$go
GO <- gopher(Seedling_High, url="athaliana", alpha=2)
## No enrichments found in task: mapman
GO_Seedling_High <- GO$go
Add the experiment name in the GO tables
GO_AzdLow6hrs <- cbind(Description='GO_Azd6hrs', GO_AzdLow6hrs)
GO_AzdHigh6hrs <- cbind(Description='GO_Azd6hrs', GO_AzdHigh6hrs)
GO_SucHigh6hrs <- cbind(Description='GO_Suc6hrs', GO_SucHigh6hrs)
GO_SucLow6hrs <- cbind(Description='GO_Suc6hrs', GO_SucLow6hrs)
GO_PiHigh6hrs <- cbind(Description='GO_Pi6hrs', GO_PiHigh6hrs)
GO_PiLow6hrs <- cbind(Description='GO_Pi6hrs', GO_PiLow6hrs)
GO_AzdNPHigh6hrs <- cbind(Description='GO_AzdNP6hrs', GO_AzdNPHigh6hrs)
GO_AzdNPLow6hrs <- cbind(Description='GO_AzdNP6hrs', GO_AzdNPLow6hrs)
GO_AzdNSHigh6hrs <- cbind(Description='GO_AzdNS6hrs', GO_AzdNSHigh6hrs)
GO_AzdNSLow6hrs <- cbind(Description='GO_AzdNS6hrs', GO_AzdNSLow6hrs)
GO_AzdHigh24hrs <- cbind(Description='GO_Azd24hrs', GO_AzdHigh24hrs)
GO_AzdLow24hrs <- cbind(Description='GO_Azd24hrs', GO_AzdLow24hrs)
GO_SucHigh24hrs <- cbind(Description='GO_Suc24hrs', GO_SucHigh24hrs)
GO_SucLow24hrs <- cbind(Description='GO_Suc24hrs', GO_SucLow24hrs)
GO_PiHigh24hrs <- cbind(Description='GO_Pi24hrs', GO_PiHigh24hrs)
GO_PiLow24hrs <- cbind(Description='GO_Pi24hrs', GO_PiLow24hrs)
GO_AzdNPHigh24hrs <- cbind(Description='GO_AzdNP24hrs', GO_AzdNPHigh24hrs)
GO_AzdNPLow24hrs <- cbind(Description='GO_AzdNP24hrs', GO_AzdNPLow24hrs)
GO_AzdNSHigh24hrs <- cbind(Description='GO_AzdNS24hrs', GO_AzdNSHigh24hrs)
GO_AzdNSLow24hrs <- cbind(Description='GO_AzdNS24hrs', GO_AzdNSLow24hrs)
GO_Seedling_High <- cbind(Description='GO_Seedling', GO_Seedling_High)
GO_Seedling_Low <- cbind(Description='GO_Seedling', GO_Seedling_Low)
Combine the GO tables
Prepare the tables
combined_up <- rbind.fill(GO_AzdHigh6hrs, GO_AzdNPHigh6hrs, GO_AzdNSHigh6hrs, GO_PiHigh6hrs, GO_SucHigh6hrs,GO_AzdHigh24hrs, GO_AzdNPHigh24hrs, GO_AzdNSHigh24hrs, GO_PiHigh24hrs, GO_SucHigh24hrs,GO_Seedling_High)
combined_down <- rbind.fill(GO_AzdLow6hrs,GO_SucLow6hrs,GO_PiLow6hrs,GO_AzdNPLow6hrs,GO_AzdNSLow6hrs,GO_AzdLow24hrs,GO_SucLow24hrs,GO_PiLow24hrs,GO_AzdNPLow24hrs,GO_AzdNSLow24hrs,GO_Seedling_Low)
Keep only the biological processes
combined_up <- combined_up[combined_up$namespace == "BP",]
combined_down <- combined_down[combined_down$namespace == "BP",]
Combining Up and Down-regulated genes together
combined_up[,"Direction"] <- "Induced"
combined_down[,"Direction"] <- "Repressed"
combined_all_up_and_down <- rbind(combined_up, combined_down)
- Export the obtained data.frame containing also the non-significant GOs
write.table(combined_all_up_and_down,file="GOs_also_NON_sgnificant_GOs.txt", quote = F ,sep = "\t", row.names=FALSE)
Removing the root terms
exclude <- c("GO:0008150", "GO:0008283", "GO:0032502", "GO:0044848", "GO:0032501", "GO:0098743", "GO:0008152", "GO:0051704", "GO:0007610", "GO:0000003", "GO:0009987",
'GO:0006791', 'GO:0001906', 'GO:0002376', 'GO:0006794', 'GO:0009758', 'GO:0015976', 'GO:0019740', 'GO:0022414',
'GO:0022610', 'GO:0023052', 'GO:0040007', 'GO:0040011', 'GO:0043473', 'GO:0048511', 'GO:0048518', 'GO:0048519', 'GO:0050789', 'GO:0050896', 'GO:0051179', 'GO:0065007', 'GO:0071840', 'GO:0098754', 'GO:0110148')
combined_all_up_and_down <- combined_all_up_and_down[! combined_all_up_and_down$id %in% exclude,]
# ' ## Change the p-values to change all the ones that are non-significant
combined_all_up_and_down$padj[combined_all_up_and_down$padj > 0.05] <- NA #Change this value as wished (normally 0.05)
Create a list of interesting GO
- Create a list of cell cycle related GO enriched in Repressed genes after 24hrs of Pi starvation
C_Cycle <- c("GO:0007049","GO:0051726","GO:0044770","GO:0007051","GO:0007059","GO:0042549","GO:0051301","GO:0051304",
"GO:0009061","GO:0007017","GO:0046490","GO:0006720","GO:0032196")
- Pyrimidine-containing compound metabolism
Pyrimidine <- c("GO:0072527",'GO:0006304','GO:0055086','GO:0018193','GO:0016072','GO:0090501','GO:0006354',
'GO:1901564','GO:1901566','GO:0006139','GO:0000375','GO:0043603','GO:0032446','GO:0019318','GO:0006259',
'GO:0006260','GO:0090305','GO:0006518','GO:0006553','GO:0006090','GO:0006089',
'GO:0008213','GO:0006396','GO:0034641','GO:0005991','GO:0009451','GO:0034660')
Replication <- c('GO:0006260','GO:0006304','GO:0090066','GO:0055086','GO:0018193','GO:0048519','GO:0006793',
'GO:0031323','GO:0045814','GO:0006270','GO:0006275','GO:0018205','GO:0016072','GO:0044260',
'GO:0090501','GO:0009069','GO:0050789','GO:1901576','GO:0046483','GO:1901564','GO:0051338',
'GO:0006139','GO:0043603','GO:0032446','GO:0006725','GO:0019318','GO:0006259',
'GO:0010498','GO:0006518','GO:0010467','GO:0033559','GO:0006090','GO:0043412','GO:0008213',
'GO:0060249','GO:0040029','GO:0009892','GO:0040008','GO:0072527','GO:0034641',
'GO:0005991','GO:0009451','GO:0034660')
- Lipopolysaccharide metabolism (repressed by sugar starvation after 24 hrs)
LPS <- c("GO:1903509","GO:1901137","GO:0006643","GO:0006629")
- Response to heat (repressed by sugar starvation after 24 hrs)
heat <- c("GO:0009408","GO:0071496","GO:0009642","GO:0016036","GO:0006950","GO:0006979","GO:1901700","GO:0002215")
- ncRNA (induced by 24hrs of sugar starvation)
ncRNA <- c('GO:0034660','GO:0042537','GO:0009768','GO:0055070','GO:0043900','GO:0051246','GO:0018198','GO:0017014',
'GO:0016054','GO:0016070','GO:0016072','GO:0042592','GO:0022900','GO:0055114','GO:0006081','GO:0006082',
'GO:0008219','GO:0009069','GO:0009308','GO:0001505','GO:0006396','GO:1901605','GO:0030258','GO:0044283',
'GO:0009850','GO:0044281','GO:0005991','GO:0005997','GO:0042430','GO:0051174','GO:0065008','GO:1901657','GO:0006766')
myList <- list(C_Cycle,Pyrimidine,Replication,LPS, heat, ncRNA)
List of GO groups overrepresented among genes induced after 24hrs of Suc starvation
aging <- c("GO:0007568","GO:0090558","GO:0048366","GO:0010618","GO:0007275")
response_to_red_light <- c("GO:0010114","GO:1901700","GO:0009743","GO:0006290","GO:0080021","GO:0017085","GO:0043617","GO:0034285","GO:0009637","GO:0009646","GO:0009611","GO:0010033")
photosynthesis <- "GO:0015979"
response_to_stimulus <- "GO:0050896"
localization <- "GO:0051179"
multi_organism_process <- "GO:0051704"
biological_regulation <- "GO:0065007"
catabolism <- "GO:0009056"
plastid_organization <- c("GO:0009657","GO:0043933","GO:0072657","GO:0022613","GO:0008643","GO:0044085","GO:0010256")
isoprenoid_transport <- c("GO:0046864","GO:0055085","GO:0006811","GO:0015850","GO:0032879","GO:0015853","GO:0072511","GO:0010232","GO:0015672","GO:0015718")
drug_metabolism <- "GO:0017144"
multidimensional_cell_growth <- "GO:0009825"
generation_of_precursor_metabolites_and_energy <- "GO:0006091"
secondary_metabolism <- c("GO:0019748","GO:0015977")
ROS_metabolism <- "GO:0072593"
sulfur_compound_biosynthesis <- "GO:0044272"
dephosphorylation <- c("GO:0016311","GO:0006733","GO:0006739")
sulfur_compound_metabolism <- "GO:0006790"
ncRNA_metabolism <- c("GO:0034660","GO:0042537","GO:0009768","GO:0055070","GO:0043900","GO:0006520","GO:0051246","GO:0018198","GO:0017014","GO:0048583","GO:0016070","GO:0016072","GO:0042592","GO:0033559","GO:0022900","GO:0055114","GO:0006081","GO:0006082","GO:0008219","GO:0009311","GO:0009069","GO:0009308","GO:0001505","GO:0006396","GO:0009850","GO:0044283","GO:0044281","GO:0009607","GO:0005991","GO:0044093","GO:0005997","GO:0042430","GO:0051174","GO:0065008","GO:0042221","GO:0006766")
cofactor_metabolism <- c("GO:0051186","GO:0006793")
carbohydrate_metabolism <- "GO:0005975"
ureide_metabolism <- "GO:0010135"
oxidative_photosynthetic_carbon_pathway <- "GO:0009854"
myList <- list(
aging = aging,
response_to_red_light= response_to_red_light,
photosynthesis=photosynthesis,
catabolism=catabolism,
plastid_organization=plastid_organization,
isoprenoid_transport=isoprenoid_transport,
drug_metabolism=drug_metabolism,
multidimensional_cell_growth=multidimensional_cell_growth,
generation_of_precursor_metabolites_and_energy=generation_of_precursor_metabolites_and_energy,
secondary_metabolism=secondary_metabolism,
ROS_metabolism=ROS_metabolism,
sulfur_compound_biosynthesis=sulfur_compound_biosynthesis,
dephosphorylation=dephosphorylation,
sulfur_compound_metabolism=sulfur_compound_metabolism,
ncRNA_metabolism=ncRNA_metabolism,
cofactor_metabolism=cofactor_metabolism,
carbohydrate_metabolism=carbohydrate_metabolism,
ureide_metabolism=ureide_metabolism,
oxidative_photosynthetic_carbon_pathway=oxidative_photosynthetic_carbon_pathway)
List of GO groups overrepresented under the different conditions
LowSuc6hr <- GO_SucLow6hrs$id[GO_SucLow6hrs$padj <= 0.05]
LowPi6hr <- GO_PiLow6hrs$id[GO_PiLow6hrs$padj <= 0.05]
LowAzd6hr <- GO_AzdLow6hrs$id[GO_AzdLow6hrs$padj <= 0.05]
LowAzdSuc6hr <- GO_AzdNPLow6hrs$id[GO_AzdNPLow6hrs$padj <= 0.05]
LowAzdPi6hr <- GO_AzdNSLow6hrs$id[GO_AzdNSLow6hrs$padj <= 0.05]
HighSuc6hr <- GO_SucHigh6hrs$id[GO_SucHigh6hrs$padj <= 0.05]
HighPi6hr <- GO_PiHigh6hrs$id[GO_PiHigh6hrs$padj <= 0.05]
HighAzd6hr <- GO_AzdHigh6hrs$id[GO_AzdHigh6hrs$padj <= 0.05]
HighAzdSuc6hr <- GO_AzdNPHigh6hrs$id[GO_AzdNPHigh6hrs$padj <= 0.05]
HighAzdPi6hr <- GO_AzdNSHigh6hrs$id[GO_AzdNSHigh6hrs$padj <= 0.05]
LowSuc24hr <- GO_SucLow24hrs$id[GO_SucLow24hrs$padj <= 0.05]
LowPi24hr <- GO_PiLow24hrs$id[GO_PiLow24hrs$padj <= 0.05]
LowAzd24hr <- GO_AzdLow24hrs$id[GO_AzdLow24hrs$padj <= 0.05]
LowAzdSuc24hr <- GO_AzdNPLow24hrs$id[GO_AzdNPLow24hrs$padj <= 0.05]
LowAzdPi24hr <- GO_AzdNSLow24hrs$id[GO_AzdNSLow24hrs$padj <= 0.05]
HighSuc24hr <- GO_SucHigh24hrs$id[GO_SucHigh24hrs$padj <= 0.05]
HighPi24hr <- GO_PiHigh24hrs$id[GO_PiHigh24hrs$padj <= 0.05]
HighAzd24hr <- GO_AzdHigh24hrs$id[GO_AzdHigh24hrs$padj <= 0.05]
HighAzdSuc24hr <- GO_AzdNPHigh24hrs$id[GO_AzdNPHigh24hrs$padj <= 0.05]
HighAzdPi24hr <- GO_AzdNSHigh24hrs$id[GO_AzdNSHigh24hrs$padj <= 0.05]
LowSeedling <- GO_Seedling_Low$id[GO_Seedling_Low$padj <= 0.05]
HighSeedling <- GO_Seedling_High$id[GO_Seedling_High$padj <= 0.05]
myList <- list(LowSuc6hr = LowSuc6hr,
LowPi6hr = LowPi6hr,
LowAzd6hr= LowAzd6hr,
LowAzdSuc6hr= LowAzdSuc6hr,
LowAzdPi6hr= LowAzdPi6hr,
HighSuc6hr= HighSuc6hr,
HighPi6hr= HighPi6hr,
HighAzd6hr= HighAzd6hr,
HighAzdSuc6hr= HighAzdSuc6hr,
HighAzdPi6hr= HighAzdPi6hr,
LowSuc24hr= LowSuc24hr,
LowPi24hr= LowPi24hr,
LowAzd24hr= LowAzd24hr,
LowAzdSuc24hr= LowAzdSuc24hr,
LowAzdPi24hr= LowAzdPi24hr,
HighSuc24hr= HighSuc24hr,
HighPi24hr= HighPi24hr,
HighAzd24hr= HighAzd24hr,
HighAzdSuc24hr= HighAzdSuc24hr,
HighAzdPi24hr= HighAzdPi24hr,
LowSeedling = LowSeedling,
HighSeedling=HighSeedling
)